Shawn M Burgess

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint The zebrafish gene claudinj is essential for normal ear function and important for the formation of the otoliths
    Amanda L Hardison
    Genome Technology Branch, National Human Genome Research Institute, NIH, Building 50, Room 5537, 50 South Drive, Bethesda, MD 20892 8004, USA
    Mech Dev 122:949-58. 2005
  2. pmc trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags
    Gabriel Renaud
    Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8004, USA
    BMC Bioinformatics 15:329. 2014
  3. pmc Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins
    Jue Zeng
    Division of Hematology Oncology, Department of Medicine, University of California, Irvine, CA, USA
    Nucleic Acids Res 36:e8. 2008
  4. pmc Mutagenesis and phenotyping resources in zebrafish for studying development and human disease
    Gaurav Kumar Varshney
    Developmental Genomics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Brief Funct Genomics 13:82-94. 2014
  5. pmc Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics
    Li Chen
    Center for Molecular Therapeutics, Center for Cancer Research, Massachusetts General Hospital, and Harvard Medical School, CNY 149 Rm7308, Thirteenth St Charlestown, MA 02129, USA
    BMC Cancer 13:93. 2013
  6. pmc Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish
    Viviana E Gallardo
    Center for Genome Regulation Facultad de Ciencias, Universidad de Chile, Casilla 653 Santiago, Chile
    BMC Dev Biol 10:120. 2010
  7. pmc Using retroviruses as a mutagenesis tool to explore the zebrafish genome
    Li En Jao
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Brief Funct Genomic Proteomic 7:427-43. 2008
  8. pmc The stat3/socs3a pathway is a key regulator of hair cell regeneration in zebrafish. [corrected]
    Jin Liang
    Genome Technology Branch, and Inherited Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
    J Neurosci 32:10662-73. 2012
  9. pmc Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases
    Wuhong Pei
    Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
    Sci Rep 6:29946. 2016
  10. doi request reprint A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish
    Gaurav K Varshney
    Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Protoc 11:2357-2375. 2016

Collaborators

Detail Information

Publications28

  1. ncbi request reprint The zebrafish gene claudinj is essential for normal ear function and important for the formation of the otoliths
    Amanda L Hardison
    Genome Technology Branch, National Human Genome Research Institute, NIH, Building 50, Room 5537, 50 South Drive, Bethesda, MD 20892 8004, USA
    Mech Dev 122:949-58. 2005
    ....
  2. pmc trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags
    Gabriel Renaud
    Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8004, USA
    BMC Bioinformatics 15:329. 2014
    ..Here, we present trieFinder, a program specifically designed to rapidly map, parse, and annotate DGE tags of various lengths against cDNA and/or genomic sequence databases...
  3. pmc Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins
    Jue Zeng
    Division of Hematology Oncology, Department of Medicine, University of California, Irvine, CA, USA
    Nucleic Acids Res 36:e8. 2008
    ..Our yeast screening strategy, combined with bioinformatics approaches, will allow both detailed and high-throughput characterization of transcription factors, scalable to the analysis of all putative DNA-binding proteins...
  4. pmc Mutagenesis and phenotyping resources in zebrafish for studying development and human disease
    Gaurav Kumar Varshney
    Developmental Genomics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Brief Funct Genomics 13:82-94. 2014
    ..Given this explosion of mutagenesis resources, it is now possible to perform systematic, high-throughput phenotype analysis of all zebrafish gene knockouts. ..
  5. pmc Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics
    Li Chen
    Center for Molecular Therapeutics, Center for Cancer Research, Massachusetts General Hospital, and Harvard Medical School, CNY 149 Rm7308, Thirteenth St Charlestown, MA 02129, USA
    BMC Cancer 13:93. 2013
    ..For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance...
  6. pmc Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish
    Viviana E Gallardo
    Center for Genome Regulation Facultad de Ciencias, Universidad de Chile, Casilla 653 Santiago, Chile
    BMC Dev Biol 10:120. 2010
    ..Therefore the primordium provides both a model for studying collective directional cell migration and the differentiation of sensory cells from multipotent progenitor cells...
  7. pmc Using retroviruses as a mutagenesis tool to explore the zebrafish genome
    Li En Jao
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Brief Funct Genomic Proteomic 7:427-43. 2008
    ..Lastly, we point to some potential directions that retroviral mutagenesis might take from the lessons of studying other model organisms...
  8. pmc The stat3/socs3a pathway is a key regulator of hair cell regeneration in zebrafish. [corrected]
    Jin Liang
    Genome Technology Branch, and Inherited Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
    J Neurosci 32:10662-73. 2012
    ..2008; Zhu et al., 2008; Qin et al., 2009), we propose that the stat3/socs3 pathway is a key response in all tissue regeneration and thus an important therapeutic target for a broad application in tissue repair and injury healing...
  9. pmc Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases
    Wuhong Pei
    Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
    Sci Rep 6:29946. 2016
    ..We further demonstrated the phenotypes were caused by delays in the tissues most highly expressing the prps1 genes. ..
  10. doi request reprint A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish
    Gaurav K Varshney
    Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Protoc 11:2357-2375. 2016
    ..Realistically, two researchers can target tens to hundreds of genes per year using this protocol...
  11. pmc High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
    Gaurav K Varshney
    Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 25:1030-42. 2015
    ..Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies. ..
  12. pmc MLV integration site selection is driven by strong enhancers and active promoters
    Matthew C LaFave
    Division of Intramural Research, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8004, USA
    Nucleic Acids Res 42:4257-69. 2014
    ..The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors...
  13. pmc A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
    Gaurav K Varshney
    Developmental Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 23:727-35. 2013
    ..These fish lines establish an important milestone for zebrafish genetics research and should greatly facilitate systematic functional studies of the vertebrate genome...
  14. pmc Loss of Mgat5a-mediated N-glycosylation stimulates regeneration in zebrafish
    Wuhong Pei
    Functional and Translation Genome Branch, National Human Genome Research Institute, 9000 Rockville Pike, Building 50, Room 5537, Bethesda, MD 20892 USA
    Cell Regen (Lond) 5:3. 2016
    ..In a large-scale genetic screening, we identified mgat5a, a gene in the N-glycosylation biosynthesis pathway whose activity negatively impacts hair cell regeneration...
  15. pmc Transcriptional signature of accessory cells in the lateral line, using the Tnk1bp1:EGFP transgenic zebrafish line
    Martine Behra
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Dev Biol 12:6. 2012
    ..However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans...
  16. pmc CRISPRz: a database of zebrafish validated sgRNAs
    Gaurav K Varshney
    Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 44:D822-6. 2016
    ..CRISPRz can be searched using multiple inputs such as ZFIN IDs, accession number, UniGene ID, or gene symbols from zebrafish, human and mouse. ..
  17. pmc Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion
    Viviana E Gallardo
    Developmental Genomics Section, Genome Technology Branch National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Dis Model Mech 8:565-76. 2015
    ..This approach demonstrates that the migrating PLLp in zebrafish can be used for large-scale, high-throughput screening for compounds that inhibit collective cell migration and, potentially, anti-metastatic compounds. ..
  18. pmc The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion
    Gaurav K Varshney
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 41:D861-4. 2013
    ..In the future, ZInC may include data from other insertional mutation projects as well. ZInC cross-references all integration data with the ZFIN (http://zfin.org/)...
  19. doi request reprint Understanding and Editing the Zebrafish Genome
    Gaurav K Varshney
    Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
    Adv Genet 92:1-52. 2015
    ....
  20. pmc GeIST: a pipeline for mapping integrated DNA elements
    Matthew C LaFave
    Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 8004, USA
    Bioinformatics 31:3219-21. 2015
    ..It has been tested on experimental data for each of these delivery vectors and fine-tuned to account for sequencing and cloning artifacts...
  21. pmc A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1
    Matthew C LaFave
    Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
    Genetics 198:167-70. 2014
    ....
  22. pmc Phoenix is required for mechanosensory hair cell regeneration in the zebrafish lateral line
    Martine Behra
    National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Genet 5:e1000455. 2009
    ..Whereas its role during early development of the lateral line remains to be addressed, in later larval stages phoenix defines a new class of proteins implicated in hair cell regeneration...
  23. pmc Disruption of the folate pathway in zebrafish causes developmental defects
    Marina S Lee
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Dev Biol 12:12. 2012
    ..The biological mechanisms through which folate prevents birth defects are not well understood. We explore the use of zebrafish as a model system to investigate the role of folate metabolism during development...
  24. pmc CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity
    Blake Carrington
    Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 43:e157. 2015
    ..This method is easy to implement by laboratories with access to a capillary sequencer. Although we validated the method using CRISPR/Cas9 and zebrafish, it can be applied to other model systems and other genome targeting nucleases. ..
  25. pmc The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure
    Jizhou Yan
    National Human Genome Research Institute, Genome Technology Branch, NIH, Bldg 50, Rm 5537, 50 South Dr, Bethesda, MD 20892, USA
    Mol Cell Biol 26:155-68. 2006
    ..On the basis of these findings, we propose that FoxI1 is capable of remodeling chromatin higher-order structure and can stably create site-specific changes in chromatin to either stably create or remove DNase I hypersensitive sites...
  26. ncbi request reprint The tip-link antigen, a protein associated with the transduction complex of sensory hair cells, is protocadherin-15
    Zubair M Ahmed
    Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland 20850, USA
    J Neurosci 26:7022-34. 2006
    ..Protocadherin-15 is therefore associated with the tip-link complex and may be an integral component of this structure and/or required for its formation...
  27. ncbi request reprint Oculofaciocardiodental and Lenz microphthalmia syndromes result from distinct classes of mutations in BCOR
    David Ng
    Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 36:411-6. 2004
    ....